Transitions of care often lead to medication errors and unnecessary healthcare utilization. Medication reconciliation has been repeatedly shown to reduce this risk. However, the great majority of evidence is limited to the provision of medication reconciliation within clinical trials and countries with well-established clinical pharmacy. Thus, this pragmatic, prospective, controlled trial evaluated the effectiveness of routine pharmacist-led medication reconciliation compared to standard care on medication errors and unplanned healthcare utilization in adult general medical patients hospitalized in a teaching hospital in Slovenia. All patients hospitalized in a ward where medication reconciliation was integrated into routine clinical practice were included in the intervention group and received admission and discharge medication reconciliation, coupled with patient counselling. The control group consisted of randomly selected patients from the remaining medical wards. The primary study outcome was unplanned healthcare utilization within 30 days of discharge, and the secondary outcomes were clinically important medication errors at hospital discharge and serious unplanned healthcare utilization within 30 days of discharge. Overall, 414 patients (53.4% male, median 71 years) were included—225 in the intervention group and 189 in the control group. In the intervention group, the number of patients with clinically important medication errors at discharge was significantly lower (intervention vs control group: 9.3% vs 61.9%). Multiple logistic regression revealed that medication reconciliation reduced the likelihood of a clinically important medication error by 20-fold, while a higher number of medications on admission was associated with an increased likelihood. However, no significant differences were noted in any and serious unplanned healthcare utilization (intervention vs control group: 33.9% vs 27.8% and 20.3% vs 14.6%, respectively). The likelihood of serious healthcare utilization increased with the age of the patient, the number of medications on admission and being hospitalized for an acute medical condition. Our pragmatic trial confirmed that medication reconciliation, even when performed as part of routine clinical practice, led to a substantial reduction in the risk of clinically important medication errors at hospital discharge but not to a reduction in healthcare utilization. Medication reconciliation is a fundamental, albeit not sufficient, element to ensure patient safety after hospital discharge.